High-throughput sequencing reveals small RNAs involved in ASGV infection

Visser, Marike; Maree, Hans J.; Rees, D. Jasper G.; Burger, Johan T.

High-throughput sequencing reveals small RNAs involved in ASGV infection

dc.contributor.author	Visser, Marike	en_ZA
dc.contributor.author	Maree, Hans J.	en_ZA
dc.contributor.author	Rees, D. Jasper G.	en_ZA
dc.contributor.author	Burger, Johan T.	en_ZA
dc.date.accessioned	2014-09-16T10:19:29Z
dc.date.available	2014-09-16T10:19:29Z
dc.date.issued	2014
dc.date.updated	2014-07-28T15:17:03Z
dc.description	CITATION: Visser, M., Maree, H. J., Rees, D. J. G. & Burger, J. T. 2014. High-throughput sequencing reveals small RNAs involved in ASGV infection. BMC Genomics, 15(1):568, doi:10.1186/1471-2164-15-568.	en_ZA
dc.description	The original publication is available at http://www.biomedcentral.com/1471-2164/15/568	en_ZA
dc.description	Publication of this article was funded by the Stellenbosch University Open Access Fund.	en_ZA
dc.description.abstract	Background : Plant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed two sRNA deep sequencing datasets, prepared from different RNA size fractions, to identify sRNAs involved in Apple stem grooving virus (ASGV) infection. Results sRNA analysis revealed virus-derived siRNAs (vsiRNAs) originating from two ASGV genetic variants. A vsiRNA profile for one of the ASGV variants was also generated showing an increase in siRNA production towards the 3′ end of the virus genome. Virus-derived sRNAs longer than those previously analysed were also observed in the sequencing data. Additionally, tRNA-derived sRNAs were identified and characterised. These sRNAs covered a broad size-range and originated from both ends of the mature tRNAs as well as from their central regions. Several tRNA-derived sRNAs showed differential regulation due to ASGV infection. No changes in microRNA, natural-antisense transcript siRNA, phased-siRNA and repeat-associated siRNA levels were observed. Conclusions This study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data.	en_ZA
dc.description.version	Publishers' Version	en_ZA
dc.format.extent	10 pages : illustrations	en_ZA
dc.identifier.citation	Visser, M., Maree, H. J., Rees, D. J. G. & Burger, J. T. 2014. High-throughput sequencing reveals small RNAs involved in ASGV infection. BMC Genomics, 15(1):568, doi:10.1186/1471-2164-15-568.	en_ZA
dc.identifier.issn	1471-2164 (online)
dc.identifier.other	doi:10.1186/1471-2164-15-568
dc.identifier.uri	http://hdl.handle.net/10019.1/95560
dc.language.iso	en_ZA	en_ZA
dc.publisher	BioMed Central	en_ZA
dc.rights.holder	Marike Visser et al.; licensee BioMed Central Ltd.	en_ZA
dc.subject	Plant small RNAs (sRNAs)	en_ZA
dc.subject	Apple stem grooving virus (ASGV) infection	en_ZA
dc.subject	Plant viruses control	en_ZA
dc.subject	Fruit -- Diseases and pests	en_ZA
dc.title	High-throughput sequencing reveals small RNAs involved in ASGV infection	en_ZA
dc.type	Article	en_ZA